├── .Rbuildignore ├── .covrignore ├── .gitattributes ├── .github ├── copilot-instructions.md └── workflows │ ├── ASan.yml │ ├── R-CMD-check.yml │ ├── RcppDeepState.yml │ ├── benchmark.yml │ ├── codemeta.yml │ ├── copilot-setup-steps.yml │ ├── memcheck.yml │ ├── pkgdown.yml │ ├── rchk.yml │ ├── rhub.yaml │ └── update-csl.yml ├── .gitignore ├── .lintr ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── DESCRIPTION ├── NAMESPACE ├── NEWS.md ├── R ├── AddTip.R ├── ArtificialExtinction.R ├── BigInteger.R ├── Cherries.R ├── ClusterTable.R ├── Combinatorics.R ├── Consensus.R ├── ConsistentSplits.R ├── Decompose.R ├── DropTip.R ├── ImposeConstraint.R ├── Information.R ├── KeptPaths.R ├── KeptVerts.R ├── LongBranchScore.R ├── MatchNodes.R ├── MatchStrings.R ├── PathLengths.R ├── PhyToString.R ├── RUtreebalance.R ├── RcppExports-manual.R ├── RcppExports.R ├── ReadMrBayes.R ├── ReadTntTree.R ├── Reweight.R ├── RoguePlot.R ├── SplitFunctions.R ├── Splits.R ├── Stemwardness.R ├── Support.R ├── TipTimedTree.R ├── TopologyOnly.R ├── TotalCopheneticIndex.R ├── TreeNumber.R ├── TreeTools-package.R ├── Treeness.R ├── as.matrix.R ├── as.multiPhylo.R ├── data.R ├── helper_functions.R ├── in.R ├── match.R ├── mst.R ├── parse_files.R ├── phylo.R ├── sort.R ├── split_analysis.R ├── sysdata.rda ├── tree_ancestors.R ├── tree_comparison.R ├── tree_descendants.R ├── tree_display.R ├── tree_generation.R ├── tree_information.R ├── tree_numbering.R ├── tree_properties.R ├── tree_rearrangement.R ├── tree_shape.R ├── tree_write.R └── zzz.R ├── README.md ├── TreeTools.Rproj ├── benchmark ├── _compare_results.R ├── _init.R ├── _run_benchmarks.R ├── bench-ClusterTable.R ├── bench-Consensus.R ├── bench-DropTip.R ├── bench-PathLengths.R ├── bench-Root.R ├── bench-SplitList.R ├── bench-renumber_tree.h.R ├── tr2000.rds └── tr80.rds ├── codemeta.json ├── cran-comments.md ├── data-raw ├── _double_factorials.R └── unrootedKeys.R ├── data ├── Lobo.RData ├── brewer.R ├── nRootedShapes.R ├── nUnrootedShapes.R └── unrootedKeys.rda ├── inst ├── CITATION ├── REFERENCES.bib ├── WORDLIST ├── _pkgdown.yml ├── apa-old-doi-prefix.csl ├── extdata │ ├── input │ │ ├── dataset.nex │ │ └── notes.nex │ ├── otherfolder │ │ └── empty.file │ ├── output │ │ ├── named.tre │ │ └── numbered.tre │ └── tests │ │ ├── ape-tree.nex │ │ ├── continuous.nex │ │ ├── encoding.nex │ │ ├── parse-nexus.nexus │ │ ├── taxon-notes.nex │ │ ├── tnt-bare-tree.tnt │ │ ├── tnt-dna.tnt │ │ ├── tnt-matrix.tnt │ │ ├── tnt-namedtree.tre │ │ ├── tnt-tree.tre │ │ └── tnt-trees-and-matrix.tnt └── include │ ├── TreeTools.h │ └── TreeTools │ ├── ClusterTable.h │ ├── SplitList.h │ ├── assert.h │ ├── keep_tip.h │ ├── n_cherries.h │ ├── renumber_tree.h │ ├── root_tree.h │ └── types.h ├── man-roxygen ├── LoboMods.R ├── MRS.R ├── characterNumParam.R ├── constraintParam.R ├── datasetParam.R ├── edgeLengthParam.R ├── edgeParam.R ├── exampleNodeSupport.R ├── nTipParam.R ├── outgroupTipsParam.R ├── preorderTreeParam.r ├── returnPhydat.R ├── split12Params.R ├── splitsObjectParam.R ├── tipLabelsParam.R ├── tipsForTreeGeneration.R ├── tree(s)Param.R ├── treeChild.R ├── treeNEdgeOptional.R ├── treeParam.r ├── treeParent.r └── xPhylo.R ├── man ├── AddTip.Rd ├── AncestorEdge.Rd ├── ApeTime.Rd ├── ArtificialExtinction.Rd ├── CharacterInformation.Rd ├── Cherries.Rd ├── CladeSizes.Rd ├── CladisticInfo.Rd ├── ClusterTable-methods.Rd ├── ClusterTable.Rd ├── CollapseNode.Rd ├── CompatibleSplits.Rd ├── Consensus.Rd ├── ConsensusWithout.Rd ├── ConstrainedNJ.Rd ├── Decompose.Rd ├── DescendantEdges.Rd ├── DoubleFactorial.Rd ├── DropTip.Rd ├── EdgeAncestry.Rd ├── EdgeDistances.Rd ├── EndSentence.Rd ├── ExtractTaxa.Rd ├── GenerateTree.Rd ├── Hamming.Rd ├── ImposeConstraint.Rd ├── J1Index.Rd ├── KeptPaths.Rd ├── KeptVerts.Rd ├── LabelSplits.Rd ├── LeafLabelInterchange.Rd ├── ListAncestors.Rd ├── Lobo.data.Rd ├── LongBranch.Rd ├── MRCA.Rd ├── MSTEdges.Rd ├── MakeTreeBinary.Rd ├── MatchEdges.Rd ├── MatchStrings.Rd ├── MatrixToPhyDat.Rd ├── MorphoBankDecode.Rd ├── N1Spr.Rd ├── NDescendants.Rd ├── NJTree.Rd ├── NPartitionPairs.Rd ├── NRooted.Rd ├── NSplits.Rd ├── NTip.Rd ├── NewickTree.Rd ├── Neworder.Rd ├── NodeDepth.Rd ├── NodeNumbers.Rd ├── NodeOrder.Rd ├── PairwiseDistances.Rd ├── PathLengths.Rd ├── PhyToString.Rd ├── PolarizeSplits.Rd ├── ReadCharacters.Rd ├── ReadMrBayesTrees.Rd ├── ReadTntTree.Rd ├── Renumber.Rd ├── RenumberTips.Rd ├── Reorder.Rd ├── Reweight.Rd ├── RightmostCharacter.Rd ├── RoguePlot.Rd ├── RootNode.Rd ├── RootTree.Rd ├── SampleOne.Rd ├── SortTree.Rd ├── SplitConsistent.Rd ├── SplitFrequency.Rd ├── SplitInformation.Rd ├── SplitMatchProbability.Rd ├── Splits.Rd ├── SplitsInBinaryTree.Rd ├── Stemwardness.Rd ├── Subsplit.Rd ├── Subtree.Rd ├── SupportColour.Rd ├── TipLabels.Rd ├── TipTimedTree.Rd ├── TipsInSplits.Rd ├── TopologyOnly.Rd ├── TotalCopheneticIndex.Rd ├── TreeIsRooted.Rd ├── TreeNumber.Rd ├── TreeShape.Rd ├── TreeTools-package.Rd ├── Treeness.Rd ├── TreesMatchingSplit.Rd ├── TreesMatchingTree.Rd ├── TrivialSplits.Rd ├── TrivialTree.Rd ├── Unquote.Rd ├── UnrootedTreesMatchingSplit.Rd ├── UnshiftTree.Rd ├── WriteTntCharacters.Rd ├── as.Newick.Rd ├── as.multiPhylo.Rd ├── brewer.Rd ├── dot-RandomParent.Rd ├── doubleFactorials.Rd ├── edge_to_splits.Rd ├── figures │ ├── Stemwardness.png │ ├── lifecycle-archived.svg │ ├── lifecycle-defunct.svg │ ├── lifecycle-deprecated.svg │ ├── lifecycle-experimental.svg │ ├── lifecycle-maturing.svg │ ├── lifecycle-questioning.svg │ ├── lifecycle-stable.svg │ └── lifecycle-superseded.svg ├── is.TreeNumber.Rd ├── logDoubleFactorials.Rd ├── match.Splits.Rd ├── match.multiPhylo.Rd ├── nRootedShapes.Rd ├── print.TreeNumber.Rd ├── root_on_node.Rd ├── sapply64.Rd ├── sort.multiPhylo.Rd └── xor.Rd ├── memcheck ├── examples.R ├── tests.R └── vignettes.R ├── src ├── ClusterTable.cpp ├── RcppExports-manual.cpp ├── RcppExports.cpp ├── ape_reorder.cpp ├── ape_reorder.h ├── as_newick.cpp ├── consensus.cpp ├── descendant_edges.cpp ├── int_to_tree.cpp ├── kept_vertices.cpp ├── minimum_spanning_tree.cpp ├── n_cherries.cpp ├── path_lengths.cpp ├── splits.cpp ├── splits_to_tree.cpp ├── tips_in_splits.cpp └── tree_shape.cpp ├── tests ├── benchmark │ ├── benchmark-as.splits.R │ ├── benchmark-consensus.R │ └── benchmark-preorder.R ├── figs │ └── rogueplot.svg ├── spelling.R ├── testthat.R └── testthat │ ├── _snaps │ ├── RoguePlot │ │ ├── rogueplot-poly.svg │ │ ├── rogueplot-simple.svg │ │ ├── rogueplot-trees1.svg │ │ └── rogueplot-trees2.svg │ ├── Support │ │ ├── labelsplits-nameless.svg │ │ ├── labelsplits-names.svg │ │ └── labelsplits.svg │ ├── mst │ │ └── mst-plotting.svg │ └── tree_display │ │ └── sorted-tree.svg │ ├── test-AddTip.R │ ├── test-ArtificialExtinction.R │ ├── test-BigInteger.R │ ├── test-Cherries.R │ ├── test-ClusterTable.R │ ├── test-Decompose.R │ ├── test-DropTip.R │ ├── test-ImposeConstraint.R │ ├── test-KeptPaths.R │ ├── test-KeptVerts.R │ ├── test-LongBranchScore.R │ ├── test-MatchNodes.R │ ├── test-MatchStrings.R │ ├── test-PathLengths.R │ ├── test-PhyToString.R │ ├── test-RUtreebalance.R │ ├── test-ReadMrBayes.R │ ├── test-ReadTntTree.R │ ├── test-Reweight.R │ ├── test-RoguePlot.R │ ├── test-SplitConsistent.R │ ├── test-SplitFunctions.R │ ├── test-Splits.R │ ├── test-Stemwardness.R │ ├── test-Support.R │ ├── test-TipTimedTree.R │ ├── test-TopologyOnly.R │ ├── test-TotalCopheneticIndex.R │ ├── test-TreeNumber.R │ ├── test-Treeness.R │ ├── test-as.matrix.R │ ├── test-as.multiPhylo.R │ ├── test-combinatorics.R │ ├── test-consensus.R │ ├── test-helper_functions.R │ ├── test-information.R │ ├── test-int_to_tree.cpp.R │ ├── test-match.R │ ├── test-mst.R │ ├── test-parsers.R │ ├── test-phylo.R │ ├── test-root_tree.h.R │ ├── test-sort.R │ ├── test-split_analysis.R │ ├── test-splits.cpp.R │ ├── test-tree_ancestors.R │ ├── test-tree_comparison.R │ ├── test-tree_descendants.R │ ├── test-tree_display.R │ ├── test-tree_generation-random.R │ ├── test-tree_generation.R │ ├── test-tree_information.R │ ├── test-tree_numbering.R │ ├── test-tree_properties.R │ ├── test-tree_rearrange.R │ ├── test-tree_shape.R │ ├── test-tree_write.R │ └── testdata │ └── nonPreCons.nex └── vignettes ├── filesystem-navigation.Rmd ├── load-data.Rmd └── load-trees.Rmd /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/.Rbuildignore -------------------------------------------------------------------------------- /.covrignore: -------------------------------------------------------------------------------- 1 | src/ape_reorder.h 2 | src/phangorn_bip.cpp 3 | R/zzz.R 4 | -------------------------------------------------------------------------------- /.gitattributes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/.gitattributes -------------------------------------------------------------------------------- /.github/copilot-instructions.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/.github/copilot-instructions.md -------------------------------------------------------------------------------- /.github/workflows/ASan.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/.github/workflows/ASan.yml -------------------------------------------------------------------------------- /.github/workflows/R-CMD-check.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/.github/workflows/R-CMD-check.yml -------------------------------------------------------------------------------- /.github/workflows/RcppDeepState.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/.github/workflows/RcppDeepState.yml -------------------------------------------------------------------------------- /.github/workflows/benchmark.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/.github/workflows/benchmark.yml -------------------------------------------------------------------------------- /.github/workflows/codemeta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/.github/workflows/codemeta.yml -------------------------------------------------------------------------------- /.github/workflows/copilot-setup-steps.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/.github/workflows/copilot-setup-steps.yml -------------------------------------------------------------------------------- /.github/workflows/memcheck.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/.github/workflows/memcheck.yml -------------------------------------------------------------------------------- /.github/workflows/pkgdown.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/.github/workflows/pkgdown.yml -------------------------------------------------------------------------------- /.github/workflows/rchk.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/.github/workflows/rchk.yml -------------------------------------------------------------------------------- /.github/workflows/rhub.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/.github/workflows/rhub.yaml -------------------------------------------------------------------------------- /.github/workflows/update-csl.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/.github/workflows/update-csl.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/.gitignore -------------------------------------------------------------------------------- /.lintr: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/.lintr -------------------------------------------------------------------------------- /CODE_OF_CONDUCT.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/CODE_OF_CONDUCT.md -------------------------------------------------------------------------------- /CONTRIBUTING.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/CONTRIBUTING.md -------------------------------------------------------------------------------- /DESCRIPTION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/DESCRIPTION -------------------------------------------------------------------------------- /NAMESPACE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/NAMESPACE -------------------------------------------------------------------------------- /NEWS.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/NEWS.md -------------------------------------------------------------------------------- /R/AddTip.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/R/AddTip.R -------------------------------------------------------------------------------- /R/ArtificialExtinction.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/R/ArtificialExtinction.R -------------------------------------------------------------------------------- /R/BigInteger.R: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /R/Cherries.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/R/Cherries.R -------------------------------------------------------------------------------- /R/ClusterTable.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/R/ClusterTable.R -------------------------------------------------------------------------------- /R/Combinatorics.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/R/Combinatorics.R -------------------------------------------------------------------------------- /R/Consensus.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/R/Consensus.R -------------------------------------------------------------------------------- /R/ConsistentSplits.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/R/ConsistentSplits.R -------------------------------------------------------------------------------- /R/Decompose.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/R/Decompose.R -------------------------------------------------------------------------------- /R/DropTip.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/R/DropTip.R -------------------------------------------------------------------------------- /R/ImposeConstraint.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/R/ImposeConstraint.R -------------------------------------------------------------------------------- /R/Information.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/R/Information.R -------------------------------------------------------------------------------- /R/KeptPaths.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/R/KeptPaths.R -------------------------------------------------------------------------------- /R/KeptVerts.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/R/KeptVerts.R -------------------------------------------------------------------------------- /R/LongBranchScore.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/R/LongBranchScore.R -------------------------------------------------------------------------------- /R/MatchNodes.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/R/MatchNodes.R -------------------------------------------------------------------------------- /R/MatchStrings.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/R/MatchStrings.R -------------------------------------------------------------------------------- /R/PathLengths.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/R/PathLengths.R -------------------------------------------------------------------------------- /R/PhyToString.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/R/PhyToString.R -------------------------------------------------------------------------------- /R/RUtreebalance.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/R/RUtreebalance.R -------------------------------------------------------------------------------- /R/RcppExports-manual.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/R/RcppExports-manual.R -------------------------------------------------------------------------------- /R/RcppExports.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/R/RcppExports.R -------------------------------------------------------------------------------- /R/ReadMrBayes.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/R/ReadMrBayes.R -------------------------------------------------------------------------------- /R/ReadTntTree.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/R/ReadTntTree.R -------------------------------------------------------------------------------- /R/Reweight.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/R/Reweight.R -------------------------------------------------------------------------------- /R/RoguePlot.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/R/RoguePlot.R -------------------------------------------------------------------------------- /R/SplitFunctions.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/R/SplitFunctions.R -------------------------------------------------------------------------------- /R/Splits.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/R/Splits.R -------------------------------------------------------------------------------- /R/Stemwardness.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/R/Stemwardness.R -------------------------------------------------------------------------------- /R/Support.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/R/Support.R -------------------------------------------------------------------------------- /R/TipTimedTree.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/R/TipTimedTree.R -------------------------------------------------------------------------------- /R/TopologyOnly.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/R/TopologyOnly.R -------------------------------------------------------------------------------- /R/TotalCopheneticIndex.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/R/TotalCopheneticIndex.R -------------------------------------------------------------------------------- /R/TreeNumber.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/R/TreeNumber.R -------------------------------------------------------------------------------- /R/TreeTools-package.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/R/TreeTools-package.R -------------------------------------------------------------------------------- /R/Treeness.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/R/Treeness.R -------------------------------------------------------------------------------- /R/as.matrix.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/R/as.matrix.R -------------------------------------------------------------------------------- /R/as.multiPhylo.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/R/as.multiPhylo.R -------------------------------------------------------------------------------- /R/data.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/R/data.R -------------------------------------------------------------------------------- /R/helper_functions.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/R/helper_functions.R -------------------------------------------------------------------------------- /R/in.R: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /R/match.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/R/match.R -------------------------------------------------------------------------------- /R/mst.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/R/mst.R -------------------------------------------------------------------------------- /R/parse_files.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/R/parse_files.R -------------------------------------------------------------------------------- /R/phylo.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/R/phylo.R -------------------------------------------------------------------------------- /R/sort.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/R/sort.R -------------------------------------------------------------------------------- /R/split_analysis.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/R/split_analysis.R -------------------------------------------------------------------------------- /R/sysdata.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/R/sysdata.rda -------------------------------------------------------------------------------- /R/tree_ancestors.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/R/tree_ancestors.R -------------------------------------------------------------------------------- /R/tree_comparison.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/R/tree_comparison.R -------------------------------------------------------------------------------- /R/tree_descendants.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/R/tree_descendants.R -------------------------------------------------------------------------------- /R/tree_display.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/R/tree_display.R -------------------------------------------------------------------------------- /R/tree_generation.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/R/tree_generation.R -------------------------------------------------------------------------------- /R/tree_information.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/R/tree_information.R -------------------------------------------------------------------------------- /R/tree_numbering.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/R/tree_numbering.R -------------------------------------------------------------------------------- /R/tree_properties.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/R/tree_properties.R -------------------------------------------------------------------------------- /R/tree_rearrangement.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/R/tree_rearrangement.R -------------------------------------------------------------------------------- /R/tree_shape.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/R/tree_shape.R -------------------------------------------------------------------------------- /R/tree_write.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/R/tree_write.R -------------------------------------------------------------------------------- /R/zzz.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/R/zzz.R -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/README.md -------------------------------------------------------------------------------- /TreeTools.Rproj: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/TreeTools.Rproj -------------------------------------------------------------------------------- /benchmark/_compare_results.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/benchmark/_compare_results.R -------------------------------------------------------------------------------- /benchmark/_init.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/benchmark/_init.R -------------------------------------------------------------------------------- /benchmark/_run_benchmarks.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/benchmark/_run_benchmarks.R -------------------------------------------------------------------------------- /benchmark/bench-ClusterTable.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/benchmark/bench-ClusterTable.R -------------------------------------------------------------------------------- /benchmark/bench-Consensus.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/benchmark/bench-Consensus.R -------------------------------------------------------------------------------- /benchmark/bench-DropTip.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/benchmark/bench-DropTip.R -------------------------------------------------------------------------------- /benchmark/bench-PathLengths.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/benchmark/bench-PathLengths.R -------------------------------------------------------------------------------- /benchmark/bench-Root.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/benchmark/bench-Root.R -------------------------------------------------------------------------------- /benchmark/bench-SplitList.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/benchmark/bench-SplitList.R -------------------------------------------------------------------------------- /benchmark/bench-renumber_tree.h.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/benchmark/bench-renumber_tree.h.R -------------------------------------------------------------------------------- /benchmark/tr2000.rds: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/benchmark/tr2000.rds -------------------------------------------------------------------------------- /benchmark/tr80.rds: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/benchmark/tr80.rds -------------------------------------------------------------------------------- /codemeta.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/codemeta.json -------------------------------------------------------------------------------- /cran-comments.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/cran-comments.md -------------------------------------------------------------------------------- /data-raw/_double_factorials.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/data-raw/_double_factorials.R -------------------------------------------------------------------------------- /data-raw/unrootedKeys.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/data-raw/unrootedKeys.R -------------------------------------------------------------------------------- /data/Lobo.RData: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/data/Lobo.RData -------------------------------------------------------------------------------- /data/brewer.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/data/brewer.R -------------------------------------------------------------------------------- /data/nRootedShapes.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/data/nRootedShapes.R -------------------------------------------------------------------------------- /data/nUnrootedShapes.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/data/nUnrootedShapes.R -------------------------------------------------------------------------------- /data/unrootedKeys.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/data/unrootedKeys.rda -------------------------------------------------------------------------------- /inst/CITATION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/inst/CITATION -------------------------------------------------------------------------------- /inst/REFERENCES.bib: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/inst/REFERENCES.bib -------------------------------------------------------------------------------- /inst/WORDLIST: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/inst/WORDLIST -------------------------------------------------------------------------------- /inst/_pkgdown.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/inst/_pkgdown.yml -------------------------------------------------------------------------------- /inst/apa-old-doi-prefix.csl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/inst/apa-old-doi-prefix.csl -------------------------------------------------------------------------------- /inst/extdata/input/dataset.nex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/inst/extdata/input/dataset.nex -------------------------------------------------------------------------------- /inst/extdata/input/notes.nex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/inst/extdata/input/notes.nex -------------------------------------------------------------------------------- /inst/extdata/otherfolder/empty.file: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /inst/extdata/output/named.tre: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/inst/extdata/output/named.tre -------------------------------------------------------------------------------- /inst/extdata/output/numbered.tre: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/inst/extdata/output/numbered.tre -------------------------------------------------------------------------------- /inst/extdata/tests/ape-tree.nex: -------------------------------------------------------------------------------- 1 | #NEXUS 2 | [R-package APE, Wed Jul 18 13:47:46 2018] 3 | 4 | BEGIN TAXA; 5 | END; 6 | -------------------------------------------------------------------------------- /inst/extdata/tests/continuous.nex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/inst/extdata/tests/continuous.nex -------------------------------------------------------------------------------- /inst/extdata/tests/encoding.nex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/inst/extdata/tests/encoding.nex -------------------------------------------------------------------------------- /inst/extdata/tests/parse-nexus.nexus: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/inst/extdata/tests/parse-nexus.nexus -------------------------------------------------------------------------------- /inst/extdata/tests/taxon-notes.nex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/inst/extdata/tests/taxon-notes.nex -------------------------------------------------------------------------------- /inst/extdata/tests/tnt-bare-tree.tnt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/inst/extdata/tests/tnt-bare-tree.tnt -------------------------------------------------------------------------------- /inst/extdata/tests/tnt-dna.tnt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/inst/extdata/tests/tnt-dna.tnt -------------------------------------------------------------------------------- /inst/extdata/tests/tnt-matrix.tnt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/inst/extdata/tests/tnt-matrix.tnt -------------------------------------------------------------------------------- /inst/extdata/tests/tnt-namedtree.tre: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/inst/extdata/tests/tnt-namedtree.tre -------------------------------------------------------------------------------- /inst/extdata/tests/tnt-tree.tre: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/inst/extdata/tests/tnt-tree.tre -------------------------------------------------------------------------------- /inst/extdata/tests/tnt-trees-and-matrix.tnt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/inst/extdata/tests/tnt-trees-and-matrix.tnt -------------------------------------------------------------------------------- /inst/include/TreeTools.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/inst/include/TreeTools.h -------------------------------------------------------------------------------- /inst/include/TreeTools/ClusterTable.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/inst/include/TreeTools/ClusterTable.h -------------------------------------------------------------------------------- /inst/include/TreeTools/SplitList.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/inst/include/TreeTools/SplitList.h -------------------------------------------------------------------------------- /inst/include/TreeTools/assert.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/inst/include/TreeTools/assert.h -------------------------------------------------------------------------------- /inst/include/TreeTools/keep_tip.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/inst/include/TreeTools/keep_tip.h -------------------------------------------------------------------------------- /inst/include/TreeTools/n_cherries.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/inst/include/TreeTools/n_cherries.h -------------------------------------------------------------------------------- /inst/include/TreeTools/renumber_tree.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/inst/include/TreeTools/renumber_tree.h -------------------------------------------------------------------------------- /inst/include/TreeTools/root_tree.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/inst/include/TreeTools/root_tree.h -------------------------------------------------------------------------------- /inst/include/TreeTools/types.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/inst/include/TreeTools/types.h -------------------------------------------------------------------------------- /man-roxygen/LoboMods.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man-roxygen/LoboMods.R -------------------------------------------------------------------------------- /man-roxygen/MRS.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man-roxygen/MRS.R -------------------------------------------------------------------------------- /man-roxygen/characterNumParam.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man-roxygen/characterNumParam.R -------------------------------------------------------------------------------- /man-roxygen/constraintParam.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man-roxygen/constraintParam.R -------------------------------------------------------------------------------- /man-roxygen/datasetParam.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man-roxygen/datasetParam.R -------------------------------------------------------------------------------- /man-roxygen/edgeLengthParam.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man-roxygen/edgeLengthParam.R -------------------------------------------------------------------------------- /man-roxygen/edgeParam.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man-roxygen/edgeParam.R -------------------------------------------------------------------------------- /man-roxygen/exampleNodeSupport.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man-roxygen/exampleNodeSupport.R -------------------------------------------------------------------------------- /man-roxygen/nTipParam.R: -------------------------------------------------------------------------------- 1 | #' @param nTip Integer specifying number of tips (leaves). 2 | -------------------------------------------------------------------------------- /man-roxygen/outgroupTipsParam.R: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /man-roxygen/preorderTreeParam.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man-roxygen/preorderTreeParam.r -------------------------------------------------------------------------------- /man-roxygen/returnPhydat.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man-roxygen/returnPhydat.R -------------------------------------------------------------------------------- /man-roxygen/split12Params.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man-roxygen/split12Params.R -------------------------------------------------------------------------------- /man-roxygen/splitsObjectParam.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man-roxygen/splitsObjectParam.R -------------------------------------------------------------------------------- /man-roxygen/tipLabelsParam.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man-roxygen/tipLabelsParam.R -------------------------------------------------------------------------------- /man-roxygen/tipsForTreeGeneration.R: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /man-roxygen/tree(s)Param.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man-roxygen/tree(s)Param.R -------------------------------------------------------------------------------- /man-roxygen/treeChild.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man-roxygen/treeChild.R -------------------------------------------------------------------------------- /man-roxygen/treeNEdgeOptional.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man-roxygen/treeNEdgeOptional.R -------------------------------------------------------------------------------- /man-roxygen/treeParam.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man-roxygen/treeParam.r -------------------------------------------------------------------------------- /man-roxygen/treeParent.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man-roxygen/treeParent.r -------------------------------------------------------------------------------- /man-roxygen/xPhylo.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man-roxygen/xPhylo.R -------------------------------------------------------------------------------- /man/AddTip.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/AddTip.Rd -------------------------------------------------------------------------------- /man/AncestorEdge.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/AncestorEdge.Rd -------------------------------------------------------------------------------- /man/ApeTime.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/ApeTime.Rd -------------------------------------------------------------------------------- /man/ArtificialExtinction.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/ArtificialExtinction.Rd -------------------------------------------------------------------------------- /man/CharacterInformation.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/CharacterInformation.Rd -------------------------------------------------------------------------------- /man/Cherries.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/Cherries.Rd -------------------------------------------------------------------------------- /man/CladeSizes.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/CladeSizes.Rd -------------------------------------------------------------------------------- /man/CladisticInfo.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/CladisticInfo.Rd -------------------------------------------------------------------------------- /man/ClusterTable-methods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/ClusterTable-methods.Rd -------------------------------------------------------------------------------- /man/ClusterTable.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/ClusterTable.Rd -------------------------------------------------------------------------------- /man/CollapseNode.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/CollapseNode.Rd -------------------------------------------------------------------------------- /man/CompatibleSplits.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/CompatibleSplits.Rd -------------------------------------------------------------------------------- /man/Consensus.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/Consensus.Rd -------------------------------------------------------------------------------- /man/ConsensusWithout.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/ConsensusWithout.Rd -------------------------------------------------------------------------------- /man/ConstrainedNJ.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/ConstrainedNJ.Rd -------------------------------------------------------------------------------- /man/Decompose.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/Decompose.Rd -------------------------------------------------------------------------------- /man/DescendantEdges.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/DescendantEdges.Rd -------------------------------------------------------------------------------- /man/DoubleFactorial.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/DoubleFactorial.Rd -------------------------------------------------------------------------------- /man/DropTip.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/DropTip.Rd -------------------------------------------------------------------------------- /man/EdgeAncestry.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/EdgeAncestry.Rd -------------------------------------------------------------------------------- /man/EdgeDistances.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/EdgeDistances.Rd -------------------------------------------------------------------------------- /man/EndSentence.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/EndSentence.Rd -------------------------------------------------------------------------------- /man/ExtractTaxa.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/ExtractTaxa.Rd -------------------------------------------------------------------------------- /man/GenerateTree.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/GenerateTree.Rd -------------------------------------------------------------------------------- /man/Hamming.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/Hamming.Rd -------------------------------------------------------------------------------- /man/ImposeConstraint.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/ImposeConstraint.Rd -------------------------------------------------------------------------------- /man/J1Index.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/J1Index.Rd -------------------------------------------------------------------------------- /man/KeptPaths.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/KeptPaths.Rd -------------------------------------------------------------------------------- /man/KeptVerts.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/KeptVerts.Rd -------------------------------------------------------------------------------- /man/LabelSplits.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/LabelSplits.Rd -------------------------------------------------------------------------------- /man/LeafLabelInterchange.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/LeafLabelInterchange.Rd -------------------------------------------------------------------------------- /man/ListAncestors.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/ListAncestors.Rd -------------------------------------------------------------------------------- /man/Lobo.data.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/Lobo.data.Rd -------------------------------------------------------------------------------- /man/LongBranch.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/LongBranch.Rd -------------------------------------------------------------------------------- /man/MRCA.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/MRCA.Rd -------------------------------------------------------------------------------- /man/MSTEdges.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/MSTEdges.Rd -------------------------------------------------------------------------------- /man/MakeTreeBinary.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/MakeTreeBinary.Rd -------------------------------------------------------------------------------- /man/MatchEdges.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/MatchEdges.Rd -------------------------------------------------------------------------------- /man/MatchStrings.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/MatchStrings.Rd -------------------------------------------------------------------------------- /man/MatrixToPhyDat.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/MatrixToPhyDat.Rd -------------------------------------------------------------------------------- /man/MorphoBankDecode.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/MorphoBankDecode.Rd -------------------------------------------------------------------------------- /man/N1Spr.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/N1Spr.Rd -------------------------------------------------------------------------------- /man/NDescendants.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/NDescendants.Rd -------------------------------------------------------------------------------- /man/NJTree.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/NJTree.Rd -------------------------------------------------------------------------------- /man/NPartitionPairs.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/NPartitionPairs.Rd -------------------------------------------------------------------------------- /man/NRooted.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/NRooted.Rd -------------------------------------------------------------------------------- /man/NSplits.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/NSplits.Rd -------------------------------------------------------------------------------- /man/NTip.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/NTip.Rd -------------------------------------------------------------------------------- /man/NewickTree.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/NewickTree.Rd -------------------------------------------------------------------------------- /man/Neworder.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/Neworder.Rd -------------------------------------------------------------------------------- /man/NodeDepth.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/NodeDepth.Rd -------------------------------------------------------------------------------- /man/NodeNumbers.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/NodeNumbers.Rd -------------------------------------------------------------------------------- /man/NodeOrder.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/NodeOrder.Rd -------------------------------------------------------------------------------- /man/PairwiseDistances.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/PairwiseDistances.Rd -------------------------------------------------------------------------------- /man/PathLengths.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/PathLengths.Rd -------------------------------------------------------------------------------- /man/PhyToString.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/PhyToString.Rd -------------------------------------------------------------------------------- /man/PolarizeSplits.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/PolarizeSplits.Rd -------------------------------------------------------------------------------- /man/ReadCharacters.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/ReadCharacters.Rd -------------------------------------------------------------------------------- /man/ReadMrBayesTrees.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/ReadMrBayesTrees.Rd -------------------------------------------------------------------------------- /man/ReadTntTree.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/ReadTntTree.Rd -------------------------------------------------------------------------------- /man/Renumber.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/Renumber.Rd -------------------------------------------------------------------------------- /man/RenumberTips.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/RenumberTips.Rd -------------------------------------------------------------------------------- /man/Reorder.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/Reorder.Rd -------------------------------------------------------------------------------- /man/Reweight.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/Reweight.Rd -------------------------------------------------------------------------------- /man/RightmostCharacter.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/RightmostCharacter.Rd -------------------------------------------------------------------------------- /man/RoguePlot.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/RoguePlot.Rd -------------------------------------------------------------------------------- /man/RootNode.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/RootNode.Rd -------------------------------------------------------------------------------- /man/RootTree.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/RootTree.Rd -------------------------------------------------------------------------------- /man/SampleOne.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/SampleOne.Rd -------------------------------------------------------------------------------- /man/SortTree.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/SortTree.Rd -------------------------------------------------------------------------------- /man/SplitConsistent.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/SplitConsistent.Rd -------------------------------------------------------------------------------- /man/SplitFrequency.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/SplitFrequency.Rd -------------------------------------------------------------------------------- /man/SplitInformation.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/SplitInformation.Rd -------------------------------------------------------------------------------- /man/SplitMatchProbability.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/SplitMatchProbability.Rd -------------------------------------------------------------------------------- /man/Splits.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/Splits.Rd -------------------------------------------------------------------------------- /man/SplitsInBinaryTree.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/SplitsInBinaryTree.Rd -------------------------------------------------------------------------------- /man/Stemwardness.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/Stemwardness.Rd -------------------------------------------------------------------------------- /man/Subsplit.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/Subsplit.Rd -------------------------------------------------------------------------------- /man/Subtree.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/Subtree.Rd -------------------------------------------------------------------------------- /man/SupportColour.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/SupportColour.Rd -------------------------------------------------------------------------------- /man/TipLabels.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/TipLabels.Rd -------------------------------------------------------------------------------- /man/TipTimedTree.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/TipTimedTree.Rd -------------------------------------------------------------------------------- /man/TipsInSplits.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/TipsInSplits.Rd -------------------------------------------------------------------------------- /man/TopologyOnly.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/TopologyOnly.Rd -------------------------------------------------------------------------------- /man/TotalCopheneticIndex.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/TotalCopheneticIndex.Rd -------------------------------------------------------------------------------- /man/TreeIsRooted.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/TreeIsRooted.Rd -------------------------------------------------------------------------------- /man/TreeNumber.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/TreeNumber.Rd -------------------------------------------------------------------------------- /man/TreeShape.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/TreeShape.Rd -------------------------------------------------------------------------------- /man/TreeTools-package.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/TreeTools-package.Rd -------------------------------------------------------------------------------- /man/Treeness.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/Treeness.Rd -------------------------------------------------------------------------------- /man/TreesMatchingSplit.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/TreesMatchingSplit.Rd -------------------------------------------------------------------------------- /man/TreesMatchingTree.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/TreesMatchingTree.Rd -------------------------------------------------------------------------------- /man/TrivialSplits.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/TrivialSplits.Rd -------------------------------------------------------------------------------- /man/TrivialTree.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/TrivialTree.Rd -------------------------------------------------------------------------------- /man/Unquote.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/Unquote.Rd -------------------------------------------------------------------------------- /man/UnrootedTreesMatchingSplit.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/UnrootedTreesMatchingSplit.Rd -------------------------------------------------------------------------------- /man/UnshiftTree.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/UnshiftTree.Rd -------------------------------------------------------------------------------- /man/WriteTntCharacters.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/WriteTntCharacters.Rd -------------------------------------------------------------------------------- /man/as.Newick.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/as.Newick.Rd -------------------------------------------------------------------------------- /man/as.multiPhylo.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/as.multiPhylo.Rd -------------------------------------------------------------------------------- /man/brewer.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/brewer.Rd -------------------------------------------------------------------------------- /man/dot-RandomParent.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/dot-RandomParent.Rd -------------------------------------------------------------------------------- /man/doubleFactorials.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/doubleFactorials.Rd -------------------------------------------------------------------------------- /man/edge_to_splits.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/edge_to_splits.Rd -------------------------------------------------------------------------------- /man/figures/Stemwardness.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/figures/Stemwardness.png -------------------------------------------------------------------------------- /man/figures/lifecycle-archived.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/figures/lifecycle-archived.svg -------------------------------------------------------------------------------- /man/figures/lifecycle-defunct.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/figures/lifecycle-defunct.svg -------------------------------------------------------------------------------- /man/figures/lifecycle-deprecated.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/figures/lifecycle-deprecated.svg -------------------------------------------------------------------------------- /man/figures/lifecycle-experimental.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/figures/lifecycle-experimental.svg -------------------------------------------------------------------------------- /man/figures/lifecycle-maturing.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/figures/lifecycle-maturing.svg -------------------------------------------------------------------------------- /man/figures/lifecycle-questioning.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/figures/lifecycle-questioning.svg -------------------------------------------------------------------------------- /man/figures/lifecycle-stable.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/figures/lifecycle-stable.svg -------------------------------------------------------------------------------- /man/figures/lifecycle-superseded.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/figures/lifecycle-superseded.svg -------------------------------------------------------------------------------- /man/is.TreeNumber.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/is.TreeNumber.Rd -------------------------------------------------------------------------------- /man/logDoubleFactorials.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/logDoubleFactorials.Rd -------------------------------------------------------------------------------- /man/match.Splits.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/match.Splits.Rd -------------------------------------------------------------------------------- /man/match.multiPhylo.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/match.multiPhylo.Rd -------------------------------------------------------------------------------- /man/nRootedShapes.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/nRootedShapes.Rd -------------------------------------------------------------------------------- /man/print.TreeNumber.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/print.TreeNumber.Rd -------------------------------------------------------------------------------- /man/root_on_node.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/root_on_node.Rd -------------------------------------------------------------------------------- /man/sapply64.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/sapply64.Rd -------------------------------------------------------------------------------- /man/sort.multiPhylo.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/sort.multiPhylo.Rd -------------------------------------------------------------------------------- /man/xor.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/man/xor.Rd -------------------------------------------------------------------------------- /memcheck/examples.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/memcheck/examples.R -------------------------------------------------------------------------------- /memcheck/tests.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/memcheck/tests.R -------------------------------------------------------------------------------- /memcheck/vignettes.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/memcheck/vignettes.R -------------------------------------------------------------------------------- /src/ClusterTable.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/src/ClusterTable.cpp -------------------------------------------------------------------------------- /src/RcppExports-manual.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/src/RcppExports-manual.cpp -------------------------------------------------------------------------------- /src/RcppExports.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/src/RcppExports.cpp -------------------------------------------------------------------------------- /src/ape_reorder.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/src/ape_reorder.cpp -------------------------------------------------------------------------------- /src/ape_reorder.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/src/ape_reorder.h -------------------------------------------------------------------------------- /src/as_newick.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/src/as_newick.cpp -------------------------------------------------------------------------------- /src/consensus.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/src/consensus.cpp -------------------------------------------------------------------------------- /src/descendant_edges.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/src/descendant_edges.cpp -------------------------------------------------------------------------------- /src/int_to_tree.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/src/int_to_tree.cpp -------------------------------------------------------------------------------- /src/kept_vertices.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/src/kept_vertices.cpp -------------------------------------------------------------------------------- /src/minimum_spanning_tree.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/src/minimum_spanning_tree.cpp -------------------------------------------------------------------------------- /src/n_cherries.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/src/n_cherries.cpp -------------------------------------------------------------------------------- /src/path_lengths.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/src/path_lengths.cpp -------------------------------------------------------------------------------- /src/splits.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/src/splits.cpp -------------------------------------------------------------------------------- /src/splits_to_tree.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/src/splits_to_tree.cpp -------------------------------------------------------------------------------- /src/tips_in_splits.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/src/tips_in_splits.cpp -------------------------------------------------------------------------------- /src/tree_shape.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/src/tree_shape.cpp -------------------------------------------------------------------------------- /tests/benchmark/benchmark-as.splits.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/benchmark/benchmark-as.splits.R -------------------------------------------------------------------------------- /tests/benchmark/benchmark-consensus.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/benchmark/benchmark-consensus.R -------------------------------------------------------------------------------- /tests/benchmark/benchmark-preorder.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/benchmark/benchmark-preorder.R -------------------------------------------------------------------------------- /tests/figs/rogueplot.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/figs/rogueplot.svg -------------------------------------------------------------------------------- /tests/spelling.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/spelling.R -------------------------------------------------------------------------------- /tests/testthat.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/testthat.R -------------------------------------------------------------------------------- /tests/testthat/_snaps/RoguePlot/rogueplot-poly.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/testthat/_snaps/RoguePlot/rogueplot-poly.svg -------------------------------------------------------------------------------- /tests/testthat/_snaps/RoguePlot/rogueplot-simple.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/testthat/_snaps/RoguePlot/rogueplot-simple.svg -------------------------------------------------------------------------------- /tests/testthat/_snaps/RoguePlot/rogueplot-trees1.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/testthat/_snaps/RoguePlot/rogueplot-trees1.svg -------------------------------------------------------------------------------- /tests/testthat/_snaps/RoguePlot/rogueplot-trees2.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/testthat/_snaps/RoguePlot/rogueplot-trees2.svg -------------------------------------------------------------------------------- /tests/testthat/_snaps/Support/labelsplits-nameless.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/testthat/_snaps/Support/labelsplits-nameless.svg -------------------------------------------------------------------------------- /tests/testthat/_snaps/Support/labelsplits-names.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/testthat/_snaps/Support/labelsplits-names.svg -------------------------------------------------------------------------------- /tests/testthat/_snaps/Support/labelsplits.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/testthat/_snaps/Support/labelsplits.svg -------------------------------------------------------------------------------- /tests/testthat/_snaps/mst/mst-plotting.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/testthat/_snaps/mst/mst-plotting.svg -------------------------------------------------------------------------------- /tests/testthat/_snaps/tree_display/sorted-tree.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/testthat/_snaps/tree_display/sorted-tree.svg -------------------------------------------------------------------------------- /tests/testthat/test-AddTip.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/testthat/test-AddTip.R -------------------------------------------------------------------------------- /tests/testthat/test-ArtificialExtinction.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/testthat/test-ArtificialExtinction.R -------------------------------------------------------------------------------- /tests/testthat/test-BigInteger.R: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/testthat/test-Cherries.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/testthat/test-Cherries.R -------------------------------------------------------------------------------- /tests/testthat/test-ClusterTable.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/testthat/test-ClusterTable.R -------------------------------------------------------------------------------- /tests/testthat/test-Decompose.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/testthat/test-Decompose.R -------------------------------------------------------------------------------- /tests/testthat/test-DropTip.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/testthat/test-DropTip.R -------------------------------------------------------------------------------- /tests/testthat/test-ImposeConstraint.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/testthat/test-ImposeConstraint.R -------------------------------------------------------------------------------- /tests/testthat/test-KeptPaths.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/testthat/test-KeptPaths.R -------------------------------------------------------------------------------- /tests/testthat/test-KeptVerts.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/testthat/test-KeptVerts.R -------------------------------------------------------------------------------- /tests/testthat/test-LongBranchScore.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/testthat/test-LongBranchScore.R -------------------------------------------------------------------------------- /tests/testthat/test-MatchNodes.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/testthat/test-MatchNodes.R -------------------------------------------------------------------------------- /tests/testthat/test-MatchStrings.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/testthat/test-MatchStrings.R -------------------------------------------------------------------------------- /tests/testthat/test-PathLengths.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/testthat/test-PathLengths.R -------------------------------------------------------------------------------- /tests/testthat/test-PhyToString.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/testthat/test-PhyToString.R -------------------------------------------------------------------------------- /tests/testthat/test-RUtreebalance.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/testthat/test-RUtreebalance.R -------------------------------------------------------------------------------- /tests/testthat/test-ReadMrBayes.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/testthat/test-ReadMrBayes.R -------------------------------------------------------------------------------- /tests/testthat/test-ReadTntTree.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/testthat/test-ReadTntTree.R -------------------------------------------------------------------------------- /tests/testthat/test-Reweight.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/testthat/test-Reweight.R -------------------------------------------------------------------------------- /tests/testthat/test-RoguePlot.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/testthat/test-RoguePlot.R -------------------------------------------------------------------------------- /tests/testthat/test-SplitConsistent.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/testthat/test-SplitConsistent.R -------------------------------------------------------------------------------- /tests/testthat/test-SplitFunctions.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/testthat/test-SplitFunctions.R -------------------------------------------------------------------------------- /tests/testthat/test-Splits.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/testthat/test-Splits.R -------------------------------------------------------------------------------- /tests/testthat/test-Stemwardness.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/testthat/test-Stemwardness.R -------------------------------------------------------------------------------- /tests/testthat/test-Support.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/testthat/test-Support.R -------------------------------------------------------------------------------- /tests/testthat/test-TipTimedTree.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/testthat/test-TipTimedTree.R -------------------------------------------------------------------------------- /tests/testthat/test-TopologyOnly.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/testthat/test-TopologyOnly.R -------------------------------------------------------------------------------- /tests/testthat/test-TotalCopheneticIndex.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/testthat/test-TotalCopheneticIndex.R -------------------------------------------------------------------------------- /tests/testthat/test-TreeNumber.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/testthat/test-TreeNumber.R -------------------------------------------------------------------------------- /tests/testthat/test-Treeness.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/testthat/test-Treeness.R -------------------------------------------------------------------------------- /tests/testthat/test-as.matrix.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/testthat/test-as.matrix.R -------------------------------------------------------------------------------- /tests/testthat/test-as.multiPhylo.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/testthat/test-as.multiPhylo.R -------------------------------------------------------------------------------- /tests/testthat/test-combinatorics.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/testthat/test-combinatorics.R -------------------------------------------------------------------------------- /tests/testthat/test-consensus.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/testthat/test-consensus.R -------------------------------------------------------------------------------- /tests/testthat/test-helper_functions.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/testthat/test-helper_functions.R -------------------------------------------------------------------------------- /tests/testthat/test-information.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/testthat/test-information.R -------------------------------------------------------------------------------- /tests/testthat/test-int_to_tree.cpp.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/testthat/test-int_to_tree.cpp.R -------------------------------------------------------------------------------- /tests/testthat/test-match.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/testthat/test-match.R -------------------------------------------------------------------------------- /tests/testthat/test-mst.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/testthat/test-mst.R -------------------------------------------------------------------------------- /tests/testthat/test-parsers.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/testthat/test-parsers.R -------------------------------------------------------------------------------- /tests/testthat/test-phylo.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/testthat/test-phylo.R -------------------------------------------------------------------------------- /tests/testthat/test-root_tree.h.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/testthat/test-root_tree.h.R -------------------------------------------------------------------------------- /tests/testthat/test-sort.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/testthat/test-sort.R -------------------------------------------------------------------------------- /tests/testthat/test-split_analysis.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/testthat/test-split_analysis.R -------------------------------------------------------------------------------- /tests/testthat/test-splits.cpp.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/testthat/test-splits.cpp.R -------------------------------------------------------------------------------- /tests/testthat/test-tree_ancestors.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/testthat/test-tree_ancestors.R -------------------------------------------------------------------------------- /tests/testthat/test-tree_comparison.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/testthat/test-tree_comparison.R -------------------------------------------------------------------------------- /tests/testthat/test-tree_descendants.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/testthat/test-tree_descendants.R -------------------------------------------------------------------------------- /tests/testthat/test-tree_display.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/testthat/test-tree_display.R -------------------------------------------------------------------------------- /tests/testthat/test-tree_generation-random.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/testthat/test-tree_generation-random.R -------------------------------------------------------------------------------- /tests/testthat/test-tree_generation.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/testthat/test-tree_generation.R -------------------------------------------------------------------------------- /tests/testthat/test-tree_information.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/testthat/test-tree_information.R -------------------------------------------------------------------------------- /tests/testthat/test-tree_numbering.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/testthat/test-tree_numbering.R -------------------------------------------------------------------------------- /tests/testthat/test-tree_properties.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/testthat/test-tree_properties.R -------------------------------------------------------------------------------- /tests/testthat/test-tree_rearrange.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/testthat/test-tree_rearrange.R -------------------------------------------------------------------------------- /tests/testthat/test-tree_shape.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/testthat/test-tree_shape.R -------------------------------------------------------------------------------- /tests/testthat/test-tree_write.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/testthat/test-tree_write.R -------------------------------------------------------------------------------- /tests/testthat/testdata/nonPreCons.nex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/tests/testthat/testdata/nonPreCons.nex -------------------------------------------------------------------------------- /vignettes/filesystem-navigation.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/vignettes/filesystem-navigation.Rmd -------------------------------------------------------------------------------- /vignettes/load-data.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/vignettes/load-data.Rmd -------------------------------------------------------------------------------- /vignettes/load-trees.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ms609/TreeTools/HEAD/vignettes/load-trees.Rmd --------------------------------------------------------------------------------